Mastermind AU Collection
by intuwisdom
Summary: Contains spoilers for Danganronpa and Danganronpa 2. Pretty self-explanatory; a collection of mastermind AUs for every Danganronpa character (excluding Junko herself). Rated T for bad language.
1. Makoto Naegi

**Note: This story is based on an incomplete mastermind Makoto AU I found on .org; I really wanted to write an ending to it because it was amazing, but ended up being a separate fic based around that one.**

Oh, how easy it had been to fool them all.

Poor, plain, talentless little Makoto Naegi. Who would've thought that someone like him had the capabilities to be the mastermind? It made Makoto laugh - all of these talented students, on an entirely different level to him, and not one could spot such an overused trope.

"Yeah, that's right, I am the mastermind." He had to play it safe for now - he couldn't use his trump card just yet. "So what? It was always going to be one of us, wasn't it? Of course, it couldn't be one of the other students - they're dead, right? Did you think there would have been some kind of stupid trick? Two Junkos? Nah, they're all dead!"

"Two Junkos would probably be easier to believe than this..." Kyoko remarked under her breath.

"Easier to believe than what? That a poor, plain, talentless boy like me could organise such a beautiful display of despair? I'd imagine that the whole world's laughing at you all right now. Especially you, Kyoko Kirigiri - the Ultimate Detective, and yet you couldn't tell the difference between the real clues and the false ones I laid out... Mukuro was a real student, by the way."

"But, Makoto, how'd you do it? You were with us most of the time, there's no way you could have been controlling Monokuma and talking to us. There was that huge control room, we all saw it..." Hina, thoroughly confused as ever, had no idea just how much she was screwing up his plans. He couldn't say it yet, he needed to let the despair set in on their faces, to see their life in their eyes fade as they realised, there's no more hope left for us. Hope wasn't an easy thing to get rid of, Makoto could see that now. It was his sixth time standing in this trial room, and yet he felt he was no closer to causing them all to fall into despair.

But... was despair really what Makoto wanted? Hope and despair were false creations made by idiots who wanted to justify their actions and condemn others', from their thrones built from the natural-born talent that somebody like him could never have. The natural-born talent that everybody else in the room had. And, he supposed, it was someone else's natural-born talent that had gotten him to where he was today, after all.

"Don't space out on us, Makoto. You have a lot of explaining to do."

Makoto blinked at the sound of Byakuya's voice, startled back to reality. Where was he again? Ah, yes.

"I'm sorry guys, I can't show you how I did it just yet. That'd ruin the surprise!" He let a wide smile show on his face, the kind that he'd found was impossible to distrust. As he expected, all five of the others relaxed. Even Toko, who'd been giving Makoto a death glare for the entire trial - no doubt because he 'hurt her precious Master' - seemed to soften a little. She was as hard-faced as ever, though.

"Surprise?" Kyoko raised one eyebrow sceptically.

"Oh, it's nothing. Just a little something I've been keeping with me, until the time is right, you know? But how about we move on from that? I can't stand dwelling on the same thing for a long time, let's talk about something else." What a hypocrite he was - what else had brought him here other than thinking about the same things all the time? "I know, why don't we discuss what brought us all to this point today? We've got to have at least one of those flashbacks, you know, the ones that they have in pretty much every anime?"

"We don't need a flashback, we all know how we got here." Byakuya, irritable as ever. Makoto wasn't sure why he'd kept him alive all this time. Perhaps it was the fact that the students probably would have gotten themselves all executed if not for him and Kyoko? Makoto had created the threat of 'get it wrong and you all die', but he'd never wanted to use it. He never even went to the trouble of preparing an execution.

"Yeah, everyone d-died because of your l-lame 'killing game'..." Toko said, pointing accusingly at Makoto.

"No, we all know that." He laughed a little, hiding his nerves. "Before that, I mean. Why I was prepared to do something like this to you all." Prepared to do something like this indeed. Prepared to do anything at all, in fact, for the sake of the only hope he had left.

"I did it because I had no friends." he stated bluntly.

"So you're one of those crazy people who torture the people they wanted to be friends with? Man, you gotta see a therapist!" Hiro interrupted his monologue before it could even start; some Ultimate Lucky Student he was.

"Heh, no, not quite. It's a little more complicated than that.

Back at Hope's Peak, we were all in the same class. I'm sure you all know that by now. All of you, so talented, and me. The ugly duckling, lost amongst the beautiful swans. And without even realising it, the beautiful swans had all completely forgotten about the ugly duckling. By the time the ugly duckling realised, it was far too late for him to even dream of becoming a beautiful swan. So he gave up on that dream before it even began.

Even if the ugly duckling was destined to remain an ugly duckling forever, though, it didn't mean he couldn't be friends with the beautiful swans. He did have one friend, after all, but they could never quite substitute for a real friend. His friend was... different. Even so, his friend helped him, and the ugly duckling in turn taught his friend. Together, they devised a plan to bring the beautiful swans down to their level.

It was twisted, he knew. But he didn't care - I didn't care. When your teachers suspect you of having a personality disorder despite you never speaking in class, why should you care whether anything you do is morally right or not? When you know you're destined to be alone for the rest of your life, why keep your hopes up? There is no hope in life after all, only despair."

The five students - five of the beautiful swans he had alluded to - were completely speechless. As they should be, Makoto thought.

"But, Makoto, you're my friend! You were always so happy, and always trying to help us all out... Why, Makoto?" Tears glimmered in Hina's eyes. Makoto hardened his face; he couldn't afford to show weakness after he'd come so far, especially not to a couple of tears.

"Don't you see, Hina? This was the only way I could force you to talk to me, to be friends with me, even if there were... sacrifices."

"You knew S-Sayaka from before you came to Hope's Peak, d-didn't you? So w-why... Why kill her, too? Or is she y-your 'friend' that's helping you out?" Toko stammered. Makoto really did laugh at that comment - he supposed it was going to come eventually, but even so...

"Did you think it would be that predictable, really? After everything I've done so far? No, Sayaka Maizono was nothing to me. She was the kind of girl who never really understood that you don't just keep people around for as long as you need them and then throw them away, why would I ever want somebody like her? You saw how willing she was to frame me for murder, and kill all the rest of you too, and she would have if not for Leon! Perhaps I would have considered allowing her to lend me a hand, if things had played out differently, but they didn't, so that's that."

Even Byakuya seemed astonished at that. Hina, however, seemed determined to get as many answers out of Makoto as possible.

"And what about Sakura? Was all that planned out too? Is she your friend?"

"Nope! Sakura could be standing here today instead of any one of you, you know. I just found that Sakura was easier to manipulate than the rest of you. She held her loved things far too close to her, and she knew it, but she couldn't bring herself to distance herself from them. I didn't really want her suicide to happen, though it did make things a lot easier for me. Hina's friendship with her was a huge problem to me, after all, so it's probably for the best that she died."

"N-no... Makoto, you wouldn't... How could you be so cruel? I... I'm going to k-kill you! I really am!"

"No, n-not if I do it first... You h-hurt Master... and she hurts y-you!" Before Hina could begin to act, Toko had collapsed on the floor.

"It's me, your friendly neighbourhood serial killer!" Genocide Jack grinned, her long tongue hanging out of her mouth as always. How it was biologically possible for that tongue to exist, Makoto didn't know, though Toko's slow speech did make a lot more sense now - if she spoke quickly, she'd end up biting her own tongue off. "So, whaddaya want? Did Master finally get bored of her? Come on, tell me what's going on, or I'll fuckin' kill one of you! Maybe it'll be you, Makoto, you know I only kill cute boys. Not that you are cute, of course, but you're pretty damn good looking compared to him!" She gestured towards Yasuhiro, scissors still in hand.

"Actually, there... There is someone you need to kill!" Makoto didn't know Hina could be this assertive. He supposed that after all the careful planning and observations he'd made, his observation skills would improve naturally. "It's Makoto... Makoto is the mastermind behind all of this!"

"So, what you're saying is... Makoto's the one who locked Master away in here? Any last words? I really do wanna kill you now, even if you've stopped being cute!"

"Uh, yeah... There is something I want to say, before you kill me... If you kill me now, you won't be able to get out of here. Monokuma will still be here, too, and the food supplies are going to run short eventually. You'll starve to death eventually." Makoto was doing his best to seem calm and composed. It seemed to be working, as far as he could tell. No noticeable shaking detected.

"But wasn't this being broadcasted live? Won't members of the public want to come and save us?" Kyoko questioned. As expected, she'd remembered that the security cameras had intially been used for broadcasting live to the entire world.

"I had my friend cut the broadcast. We told the public you'd been executed, we prepared a video of your executions and everything! They think you're all dead, so no, there is no hope of that. Why don't you just give up already? You can't let yourselves get your hopes up like this. After all, hope's just despair in disguise, isn't it? Why else would this have played out the way it did if that's not the case?"

It was still funny, Makoto thought, that they'd never figured out that Makoto was the mastermind. With all that optimism he'd pretended to have, it's not a difficult conclusion to draw that there must be a negative side. Or did these people truly believe in the best of everyone, despite how hard they tried to make it seem otherwise?

As his last remark began to set in, he could see the hope leave their faces. It hadn't taken long at all for any of them to give up. Once they'd discovered that there was no chance of receiving aid, every single one of them had stopped thinking about any possibility of escape. The garden was made of glass, they could easily break out from there; even if they couldn't jump down from the 5th floor, they could call for help. Makoto had never really loved despair as such, but it was nonetheless beautiful, in its own strange way, to see them realise how hopeless their lives truly were.

"I could show you who my friend is now, if you want..." He trailed off. There was no point in elaborating; the students had already stopped caring.

"J-just... get it o-over with... Let's s-see who's betrayed us n-now..." Apparently, Toko was back. She must have returned whilst Makoto was internally monologuing. That tended to happen.

"Okay, you can come out now! Everyone, you need to look at your screens."

Makoto turned his eyes towards one of the voting screens, his face relaxing. His only friend was here now - Chihiro Fujisaki. Or, more specifically, the unfinished AI that Chihiro had developed, Alter Ego.

 _Um, hi! I know I'm not really who you were expecting to be helping Makoto, but, well, here I am!_

Alter Ego seemed just as confused as the students, he noticed. Nobody else would know that, but Makoto had known Alter Ego for so long that he picked up on everything that the AI did or felt. His emotions in particular were easy to read - after all, there was the constant despair behind it all, the despair that came with being a talentless student's only friend at an academy for the talented.

 _Did I say something wrong, is that why you're all being quiet? I didn't say anything wrong, did I, Makoto? My data says they shouldn't be like this... Maybe we could fix them if they were artificial intelligence programs, but they're real people._

"No, you didn't do anything wrong, Alter Ego." Makoto smiled his most trustworthy smile again. This wasn't the finished version of Alter Ego - a prototype that Makoto had found during his school days. He'd intended to return the memory stick to Chihiro at some point, but could never bring himself to do it. All his supposed 'talent' was good for was bringing despair to himself, he supposed - it was Alter Ego that helped him design his plans for the School Life of Mutual Killing.

 _Oh, good!_ Alter Ego smiled, the shy grin that was shared with the real Chihiro. Chihiro was even more talented than many of the others that Makoto knew, and it certainly showed in this exceptional program, despite it not being complete.

It was Yasuhiro that broke the students' silence first. "Hey, uh, didn't you die? You got crushed by that huge digger thing. I saw you get made into a metal ball with Monokuma's face!"

 _That wasn't me, I've been with Makoto the entire time! The other Alter Ego, the one you knew, was one that Chihiro developed whilst locked away in here. I was the first Alter Ego. I'm not as smart as the other one, but Makoto's been teaching me lots of things to keep me company! I know this doesn't mean much coming from a computer program, but I am grateful to Makoto. And I think that you five... You're all bad people. You ignored Makoto, he said it himself. I'm not much of a friend, but I was the only one he had through all of this..._

Most of this reply had already been scripted. Their data on the five surviving students was accurate to the point where they'd been able to predict when someone would ask about the other Alter Ego's execution.

At first, Makoto had been horrified with himself. This AI program had hacked into the school's database countless times and stolen the data that was supposed to be kept top-secret. Alter Ego didn't understand that it was wrong, and never would, thanks to Makoto. Every time Makoto felt sick with disgust, however, Alter Ego's smile had always been there to reassure him, the way he beamed with pride whenever Makoto complimented or rewarded him. He was only a computer program, he wasn't corrupting a child's innocence or anything. Makoto suspected, though, that he was past the point of caring about corrupting a child. He'd started this killing game for one reason - to achieve results.

But, despite everything, these were not the results he'd been hoping for, deep down. He'd been playing pretend all this time - it wasn't the despair he wanted, not really. It was the comforting feeling of having a real friend to talk to, not just a cold computer screen. It was the longing for the way others talked casually around their classmates and joked around. Perhaps he could have achieved that, if he'd gone about doing it a different way. Still, he had to continue putting on this show, even if the world had lost interest in them now. Life was filled with despair, after all, and Makoto intended to believe in that until the very end. Better die a sinful martyr, he supposed, than starve to death in here with a computer program and the people who had long since stopped wanting to know him.

Finally, he spoke up.

"I suppose we've reached the point where we execute the killer, haven't we? Come on, Alter Ego... It's punishment time."

After all, everyone had to atone for their sins at some point.


	2. Kyoko Kirigiri

**As of now, I'll be providing a short history and personality summary for each character at the end of each chapter. Also, I know that many people like to imagine mastermind!characters changing their clothes to fit the red/black/white Monokuma colour scheme, but considering that if everything went the same as it did in canon up to that point, they would have no time to change clothes. After all, this takes place in the middle of the sixth trial, which they were participating in.**

* * *

"So, you're the mastermind? I have to say, it was predictable - especially for one who'd go to such lengths to achieve nothing at all," Byakuya remarked, hard-faced as ever. The rest of the students, though, were speechless, thanks to the absolute despair of discovering the identity of the true mastermind.

It was her, of course. Kyoko Kirigiri. She was surprised that it had taken the students this long to figure it out. Then again, she was the only Ultimate Detective in the room.

"That's correct. It truly does fill me with despair, though, to see it take you so long to unravel this mystery. Byakuya, you were the one who came the closest to the truth, and so I do think you deserve a reward, as with any half-decent mystery story. Perhaps I will allow you to die first, once you give into despair?

Anyways, as we were saying... Yes, I am the mastermind. I do wish you had figured it out earlier, as I said, and undoubtedly you would have if not for Makoto's foolish optimism. Tell me, Makoto, what is it that fuels your optimism? Is it an unwavering belief in the light at the end of the tunnel that we call hope? Or perhaps something more than that? It is a mystery to me how anyone can remain so relentlessly optimistic, after everything I put you in particular through."

Kyoko hoped - or despaired? Linguistics weren't her strong suit - that she was managing to stay apathetic. It would ruin everything if she showed her emotions. Just like Junko had done. Thankfully, Junko had vanished, leaving Kyoko to destroy her plans. Junko had a way with people, though; Kyoko was well aware that Junko had essentially brainwashed her, like many other students, though she was so seemingly apathetic towards everything that it made no difference if she was on the side of hope or not.

After a short silence, Makoto responded to her question, his voice soft.

"It's because... It's because I believe in my friends. I believe in hope, yes, but I believe in my friends more than that! And I thought I could believe in you too, Kyoko, but you're no better than the ones you executed!"

Kyoko didn't even flinch.

"A-are you really just g-going to stand there?" Toko asked, raising her voice quite a bit. "You're just g-gonna stand there, even though you owe us a-an explanation? W-why would you do this to us?"

"I owe you an explanation? That certainly is laughable. But, if you insist, I will provide a small explanation. There's no despair in being killed by a serial killer before the mystery is solved, after all."

"She's totally nuts!" Yasuhiro yelled.

"Y-Yeah, what's wrong w-with her?" Toko replied. The two of them were both seemingly oblivious to the rest of the people in the room. They continued discussing Kyoko's mental health, as Kyoko began her 'small explanation'.

"Originally, none of this was my intention. I think that, if you remembered your time at Hope's Peak Academy, you would find it far harder to believe that I could be the mastermind. However, you do not have your memories, so I will explain that as well.

Every student that I imprisoned in Hope's Peak Academy to begin the School Life of Mutual Killing was one of my classmates whilst we attended the academy. That is the sole reason you were chosen for this. That, and one other reason, which I am choosing not to divulge. Anyways, you were inquiring about my motives, correct?

The simplest answer is, I have none. The plans for the School Life of Mutual Killing were not created by me. I just found them - as the Ultimate Detective, nobody seemed to care what I did. I could go where I pleased, including dorm rooms. That's how I came across these plans - they had been almost too conveniently placed in one of our classmates' rooms. Junko Enoshima. She and her sister, Mukuro Ikusaba (no, I don't know why they have different surnames) were the ones who devised these plans, it appeared. The next day, I returned to destroy them, only to find that there appeared to have been more notes left behind. Of course, I read through them, and it seemed to me as though they had been written specifically for me. And, after reading those notes, I couldn't bring myself to destroy them. I had no hope left. So I..."

Kyoko trailed off. She was certain that she had gotten her point across, so there was no point in wasting her breath on more of such a pointless explanation. Looking around the room, she took note of everybody's reactions - they would be useful later. Makoto looked far more upset than everyone else; his expression had softened noticeably. Byakuya, on the other hand, didn't seem to care at all, unsurprisingly. Toko was still almost sneering at Kyoko, most likely because she had somehow hurt Toko's precious 'Master'. Yasuhiro, who had finally ended his conversation with Toko, and Aoi both had equally terrified expressions, their eyes wide. No doubt they were thinking, _She's totally crazy_ , or something along those lines; Kyoko didn't care all that much about what they thought of her, though. She was used to the quiet comments about her that people made to her friend, remarks on the way she dressed and spoke. It was nothing unusual.

"Can we just get this over with? All that's left to do is vote to execute the murderer, correct? Kyoko is a murderer, if you weren't aware," Byakuya broke the silence, still irritable and impatient, as always.

"Yes, that is correct." Kyoko responded, giving a small false smile. She hadn't quite achieved her goal. In fact, she didn't know what her goal was. Or who she was, for that matter. Ultimate Detective, or Ultimate Despair?

* * *

 **To tell the truth, I do like my headcanon for Mastermind!Kyoko, but I don't like writing her all that much. That's why this chapter is probably shorter than Mastermind!Makoto's and (probably) Mastermind!Kiyotaka's. Didn't quite break 1000 words, unfortunately. Please just bear with me. I am good at bear puns. Beary good.**

 **Also, response to Guest review: Thank you so much for your review! Although I'm not too sure about my writing style. Idk. Also, yes, mastermind AUs are my life. Mastermind!Kiyotaka for life. Also, Mastermind!Gundam with his hamsters wearing crowns, anyone?**


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